SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, DC 20549

SCHEDULE 13D

(Rule 13d-102)

INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT

TO RULE 13d-l(a) AND AMENDMENTS THERETO FILED PURSUANT

TO RULE 13d-2(a)

(Amendment No. 6)*

BeiGene, Ltd.

 (Name of Issuer)

Ordinary Shares, par value $0.0001 per share

(Title of Class of Securities)

07725L102**

(CUSIP number)

Alexandra A. Toohey

Chief Financial Officer

Baker Bros. Advisors LP

860 Washington Street, 3^rd Floor

New York, NY 10014

(212) 339-5690

(Name, address and telephone number of person authorized to receive notices and communications)

January 2, 2020

(Date of event which requires filing of this statement)

If the filing person has previously filed a statement on Schedule 13G to report the acquisition that is the subject of this Schedule 13D, and is filing this schedule because of Rule 13d-1(e), 13d-1(f) or 13d-1(g), check the following box ¨.

(Continued on the following pages)

(Page 1 of 10 Pages)

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*The remainder of this cover page shall be filled out for a reporting person’s initial filing on this form with respect to the subject class of securities, and for any subsequent amendment containing information which would alter disclosures provided in a prior cover page.

The information required on the remainder of this cover page shall not be deemed to be “filed” for the purpose of Section 18 of the Securities Exchange Act of 1934 or otherwise subject to the liabilities of that section of the Act but shall be subject to all other provisions of the Act.

**This CUSIP applies to the American Depositary Shares, each representing thirteen Ordinary Shares

(1) Includes 153,104,705 of the Ordinary Shares of BeiGene, Ltd. (the “Issuer”) reported that are beneficially owned through American Depositary Shares (“ADS”), 18,564 Ordinary Shares underlying restricted stock units of the Issuer (“RSU’s”) and 301,522 Ordinary Shares underlying 301,522 options. Each ADS represents 13 Ordinary Shares of the Issuer.

(2) Based on 1,007,975,711 Ordinary Shares outstanding at January 2, 2020 as reported in the Issuer’s Form 8-K filed with the Securities and Exchange Commission (“SEC”) on January 2, 2020.

(1) Includes 153,104,705 Ordinary Shares reported that are beneficially owned through ADS, 18,564 Ordinary Shares underlying RSU’s and 301,522 Ordinary Shares underlying 301,522 options. Each ADS represents 13 Ordinary Shares of the Issuer.

(2) Based on 1,007,975,711 Ordinary Shares outstanding at January 2, 2020 as reported in the Issuer’s Form 8-K filed with the SEC on January 2, 2020.

(1) Includes 153,502,479 Ordinary Shares reported that are beneficially owned through ADS, 18,564 Ordinary Shares underlying RSU’s, 301,522 Ordinary Shares underlying 301,522 options, 92,326 Ordinary Shares (7,102 in the form of ADS) received from an in-kind pro rata distribution in October 2017 and 218,817 Ordinary Shares (13,516 in the form of ADS) received from an in-kind pro rata distribution in June 2019. Each ADS represents 13 Ordinary Shares of the Issuer.

(2) Based on 1,007,975,711 Ordinary Shares outstanding at January 2, 2020 as reported in the Issuer’s Form 8-K filed with the SEC on January 2, 2020.

(1) Includes 153,502,479 Ordinary Shares reported that are beneficially owned through ADS, 18,564 Ordinary Shares underlying RSU’s, 301,522 Ordinary Shares underlying 301,522 options, 92,326 Ordinary Shares (7,102 in the form of ADS) received from an in-kind pro rata distribution in October 2017 and 218,817 Ordinary Shares (13,516 in the form of ADS) received from an in-kind pro rata distribution in June 2019. Each ADS represents 13 Ordinary Shares of the Issuer.

(2) Based on 1,007,975,711 Ordinary Shares outstanding at January 2, 2020 as reported in the Issuer’s Form 8-K with the SEC on January 2, 2020.

Amendment No. 6

This Amendment No. 6 to Schedule 13D amends and supplements the previously filed Schedules 13D filed by Baker Bros. Advisors LP (the “Adviser”), Baker Bros. Advisors (GP), LLC (the “Adviser GP”), Julian C. Baker, Felix J. Baker and FBB3 LLC (“FBB3”) (collectively the “Reporting Persons”). Except as supplemented herein, such statements, as heretofore amended and supplemented, remain in full force and effect.

The Adviser GP is the sole general partner of the Adviser. Pursuant to the management agreements, as amended, among the Adviser, Baker Brothers Life Sciences, L.P. (“Life Sciences”) and 667, L.P. (“667”, and together with Life Sciences, the “Funds”), and their respective general partners, the Funds’ respective general partners relinquished to the Adviser all discretion and authority with respect to the investment and voting power over securities held by the Funds, and thus the Adviser has complete and unlimited discretion and authority with respect to the Funds’ investments and voting power over investments.

Item 4 of Schedule 13D is supplemented and amended, as the case may be, as follows:

On January 2, 2020, concurrent with the effectiveness of the collaboration agreement between the Issuer, a wholly-owned subsidiary of BeiGene, Inc. (the “Issuer”), BeiGene Switzerland GmbH, and Amgen Inc. (“Amgen”) and following the approval by a majority vote of the Issuer’s shareholders, the Issuer closed the sale of 206,635,013 ordinary shares of the Issuer (“Ordinary Shares”) to Amgen in the form of 15,895,001 American Depositary Shares of the Issuer (“ADS”). Each ADS represents 13 Ordinary Shares of the Issuer. The above described ADS issued to Amgen represent approximately 20.5% of the Issuer’s issued and outstanding Ordinary Shares which resulted in the decreases in percentage of beneficial ownership of the Reporting Persons reflected on the cover pages of this Amendment No. 6 and in Item 5 below.

The Funds hold securities of the Issuer for investment purposes. The Reporting Persons or their affiliates may purchase additional securities or dispose of securities in varying amounts and at varying times depending upon the Reporting Persons’ continuing assessments of pertinent factors, including the availability of shares of common stock or other securities for purchase at particular price levels, the business prospects of the Issuer, other business investment opportunities, economic conditions, stock market conditions, money market conditions, the attitudes and actions of the board of directors of the Issuer (the “Board”) and management of the Issuer, the availability and nature of opportunities to dispose of securities of the Issuer and other plans and requirements of the particular entities. The Reporting Persons may discuss items of mutual interest with the Issuer, which could include items in subparagraphs (a) through (j) of Schedule 13D.

Depending upon their assessments of the above factors, the Reporting Persons or their affiliates may change their present intentions as stated above and they may assess whether to make suggestions to the management of the Issuer regarding financing, and whether to acquire additional securities of the Issuer (by means of open market purchases, privately negotiated purchases, or otherwise) or to dispose of some or all of the securities of the Issuer under their control.

Except as otherwise disclosed herein, at the present time, the Reporting Persons do not have any plans or proposals with respect to any extraordinary corporate transaction involving the Issuer including, without limitation, those matters described in subparagraphs (a) through (j) of Item 4 of Schedule 13D.

Item 5 of this Schedule 13D is hereby amended and restated as follows:

(a) and (b) Items 7 through 11 and 13 of each of the cover pages of this Amendment No. 6 are incorporated herein by reference.

Set forth below is the aggregate number of Ordinary Shares directly held by the Funds, 153,104,705 of which are directly held by the Funds through ADS, along with the percentage of the Issuer’s outstanding Ordinary Shares such holdings represent. The information set forth below is based on 1,007,975,711 Ordinary Shares outstanding at January 2, 2020 as reported in the Issuer’s Form 8-K with the Securities and Exchange Commission (“SEC”) on January 2, 2020. Such percentage figures are calculated in accordance with Rule 13d-3 under the Securities Exchange Act of 1934, as amended.

Michael Goller and Ranjeev Krishana, full-time employees of the Adviser, have served on the Board since April 21, 2015 and October 7, 2014, respectively. Prior to serving on the Board, Michael Goller was a Board observer. Michael Goller and Ranjeev Krishana currently serve on the Board as representatives of the Funds. Michael Goller and Ranjeev Krishana each hold 282,035 options to purchase Ordinary Shares (“Stock Options”) received in connection with their service on the Board, 150,761 of which are vested as of 60 days from the date of this Amendment No. 6. Michael Goller and Ranjeev Krishana each hold 9,282 Restricted Stock Units (“RSU’s”) in connection with their service on the Board. The RSU’s are vested as of the date of this Amendment No. 6. The policy of the Funds and the Adviser does not permit managing members of the Adviser GP or full-time employees of the Adviser to receive compensation for serving as directors of the Issuer, and the Funds are instead entitled to the pecuniary interest in any compensation received for their service.

The Adviser GP, Felix J. Baker and Julian C. Baker as managing members of the Adviser GP, and the Adviser may be deemed to be beneficial owners of securities of the Issuer directly held by the Funds.

Julian C. Baker and Felix J. Baker are also the sole managers of FBB3 and by policy they do not transact in or vote the securities of the Issuer held by FBB3.

(c) Except as disclosed herein, none of the Reporting Persons or their affiliates has effected any other transactions in securities of the Issuer during the past 60 days.

(d) Certain securities of the Issuer are held directly by 667, a limited partnership the sole general partner of which is Baker Biotech Capital, L.P., a limited partnership the sole general partner of which is Baker Biotech Capital (GP), LLC. Julian C. Baker and Felix J. Baker are the managing members of Baker Biotech Capital (GP), LLC.

Certain securities of the Issuer are held directly by Life Sciences, a limited partnership the sole general partner of which is Baker Brothers Life Sciences Capital, L.P., a limited partnership the sole general partner of which is Baker Brothers Life Sciences Capital (GP), LLC. Julian C. Baker and Felix J. Baker are the managing members of Baker Brothers Life Sciences Capital (GP), LLC.

(e) Not applicable.

SIGNATURE

After reasonable inquiry and to the best of my knowledge and belief, I certify that the information set forth in this statement is true, complete and correct.

January 7, 2020